Typically in Northern climates the inner cover and telescopic cover are the norm. The advantage is the double lid cuts down on condensation in winter. Typically in the South and in migratory beekeeping they use the migratory cover. Partly because the condensation isn't so big a problem in the South and, as mentioned, you can stack the hives up against each other.
I'm in the North and I decided I was tired of feeding the skunks and mice, so I went to all upper entrances. I nailed a board across the entrance to the SBB and put a migratory cover on with some shims to make the entrance (yes the warm way). It looks like this:http://incolor.inetnebr.com/bush/images/MigratoryTopEntrance2.JPG
I closed off about half to three fourths of the opening on most of them with a piece of lath or screen molding or just a ripped piece off of a one by and I put a piece of foam on top with the bricks holding it on. They seemed to do fine with the moist air escaping through the upper entrance and the foam to keep the wood on top from being cold. Condensation occurs when the moisture builds up in the top and the top is cold enough to cause the moisture in the warmer air to condense on the colder lid (like water on the side of a cold glass). This has worked well for me.
I make a lot of my own covers out of 3/4" plywood. The plywood stays flat better and the 3/4" is heavy enough to not blow off so easily.